edpiecepoint(1)                                                edpiecepoint(1)

       edpiecepoint - edit a list of piece coordinates

       edpiecepoint  [options] [input_file] output_file

       This program allows one to "edit" a list of piece coordinates, or a
       list of integer point coordinates, in three ways: 1) The set of Z val-
       ues may be mapped, one-to-one, to any arbitrary new set of Z values;
       and 2) The X, Y or Z coordinates of all pieces or points may be shifted
       by a constant.  3) The overlap between pieces can be changed.  In addi-
       tion, one can create a new piece list for single frame images or mon-
       taged images.  The pieces can be ordered in rows, in columns, or even
       progressing in Z first for each montage position.

       The remapping of Z values is specified by a list of values (comma-sepa-
       rated ranges, e.g. 0-3,5-7).  This list must have the same number of Z
       values as in the input list of Z values.  The Z values in the input
       list will be mapped one-to-one onto the new list.  Enter "/" to take
       the input list without modification Enter numbers between -999 and -990
       to delete points with a particular Z value; e.g. if the input list has
       Z values from 0 to 9, entering 0-4,-999,5-8 will delete all points with
       Z between 4.5 and 5.5, and shift the Z of points with Z greater then
       5.5 down by 1.  If the input list has Z from 0-19, entering
       0-9,-999--990 will remove all points with Z from 10 to 19.  Enter -1 to
       replace each Z value with its negative.

       When you create a new piece list, you control the overlap between
       pieces by entering a spacing instead.  This spacing is the frame size
       minus the overlap; e.g., for a size of 2048 and an overlap of 10%, one
       would enter 2048 - 204 = 1844.  Spacing can be measured by taking the
       difference between the coordinates of corresponding points in adjacent
       pieces.  For example, if a feature is at an X coordinate of 1800 in one
       piece and at 100 in the piece to the right, then the spacing in X is
       1800 - 100 = 1700.  Enter a negative number for X spacing if pieces are
       ordered from right to left, or a negative number for Y spacing if
       pieces are ordered from top to bottom.  Enter / if you just have one

       Edpiecepoint uses the PIP package for input (see the manual page for
       pip) and can still take sequential input interactively.  The follow-
       ing options can be specified either as command line arguments (with the
       -) or one per line in a command file or parameter file (without the -).
       Options can be abbreviated to unique letters; the currently valid
       abbreviations for short names are shown in parentheses.

       -input (-i) OR -InputFile      File name
              Input piece list or point file.  If this option is not entered
              and -create is not entered, the first non-optional argument will
              be used for an input file.

       -output (-ou) OR -OutputFile   File name
              Output piece list or point file.  If this option is not entered,
              the second non-optional argument will be used if -create is not
              entered; otherwise the first non-option argument will be used
              for an output file.

       -create (-cr) OR -CreateForSections      Integer
              Number of sections to create a new piece list for

       -pieces (-pi) OR -PiecesInXandY     Two integers
              Number of pieces in X and Y in the newly created piece list

       -spacing (-sp) OR -SpacingInXandY   Two integers
              Spacing between the pieces in X and Y in the newly created piece
              list.  Enter the negative of a spacing to have pieces coordi-
              nates put out in inverse order, from high to low coordinates.
              For how to determine the desired spacing, see above.

       -columns (-co) OR -ColumnsOfPieces
              Order pieces in a newly created piece list so that successive
              pieces occur in columns (in Y) rather than in rows (in X).

       -stacks (-st) OR -StacksOfPieces    Integer
              Order pieces in a newly created piece list so that successive
              pieces go through the entire set of Z values at each position in
              X and Y.  Enter 1 to have pieces in order by Z, or -1 for pieces
              in inverse order.  This option can be used together with the
              -columns option.

       -divide (-d) OR -DivideByBinning    Integer
              This option can be used to make a new piece list that works with
              binned images.  Rather than just dividing the existing coordi-
              nates by the binning, the program determines a new overlap value
              and makes sure that coordinates are regularly spaced apart.  To
              do this, it needs the image sizes before and after binning,
              entered with -size and -binned.

       -overlap (-ov) OR -NewOverlapInXandY     Two integers
              This option can be used to change the overlap between pieces in
              a piece list.  Enter the new overlaps in X and Y, and enter the
              size of the pieces with the -size option.

       -size (-si) OR -SizeInXandY    Two integers
              Size of pieces in X and Y.  This entry is required to adjust
              overlap or to divide by binning; in the latter case enter the
              full size of the unbinned images to which the input piece list

       -binned (-b) OR -BinnedSizeInXandY       Two integers
              New, binned size of pieces in X and Y (required to divide by

       -new (-n) OR -NewZList    List of integer ranges
              List of Z values to map old list to.  There must be as many val-
              ues in this list as in the list of Z values to remap.  See notes
              above on the contents of this list.

       -add (-a) OR -AddToAllCoordinates   Three floats
              Amount to add to all coordinates in X, Y, and Z, after remapping

       -param (-pa) OR -ParameterFile      Parameter file
              Read parameter entries as keyword-value pairs from a parameter

       -help (-h) OR -usage
              Print help output

              Read parameter entries from standard input.

       If there are no command-line arguments, Edpiecepoint takes sequential
       input the old way, with the following entries:

       Name of input piece or point list file, or Return if none

       IF you enter "Return", then the program will create a new piece
          list.  Then make the following 4 entries:

          Number of sections (N) for which to make piece coordinates.  The Z
            coordinates will initially run from 0 to N-1, and the lower left X
            and Y coordinates will be 0.

          Number of pieces in X and in Y (enter / for 1,1)

          Spacing between pieces in X and in Y.  See above.

          0 if pieces progress along rows in the image file, or 1 if they
          progress along columns.

       Name of output piece or point list file

       New list of Z values.  See above.

       Amounts to add to all X, Y, and Z coordinates.  These values will be
          added after the remapping of Z values, if any.

       Written by David Mastronarde, 5/8/89

       Email bug reports to mast at colorado dot edu.

IMOD                                 4.9.5                     edpiecepoint(1)